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Reed JN, Huang J, Li Y, Ma L, Banka D, Wabitsch M, Wang T, Ding W, Björkegren JL, Civelek M. Systems genetics analysis of human body fat distribution genes identifies adipocyte processes. Life Sci Alliance 2024; 7:e202402603. [PMID: 38702075 PMCID: PMC11068934 DOI: 10.26508/lsa.202402603] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2024] [Revised: 04/19/2024] [Accepted: 04/22/2024] [Indexed: 05/06/2024] Open
Abstract
Excess abdominal fat is a sexually dimorphic risk factor for cardio-metabolic disease and is approximated by the waist-to-hip ratio adjusted for body mass index (WHRadjBMI). Whereas this trait is highly heritable, few causal genes are known. We aimed to identify novel drivers of WHRadjBMI using systems genetics. We used two independent cohorts of adipose tissue gene expression and constructed sex- and depot-specific Bayesian networks to model gene-gene interactions from 8,492 genes. Using key driver analysis, we identified genes that, in silico and putatively in vitro, regulate many others. 51-119 key drivers in each network were replicated in both cohorts. In other cell types, 23 of these genes are found in crucial adipocyte pathways: Wnt signaling or mitochondrial function. We overexpressed or down-regulated seven key driver genes in human subcutaneous pre-adipocytes. Key driver genes ANAPC2 and RSPO1 inhibited adipogenesis, whereas PSME3 increased adipogenesis. RSPO1 increased Wnt signaling activity. In differentiated adipocytes, MIGA1 and UBR1 down-regulation led to mitochondrial dysfunction. These five genes regulate adipocyte function, and we hypothesize that they regulate fat distribution.
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Affiliation(s)
- Jordan N Reed
- https://ror.org/0153tk833 Department of Biomedical Engineering, University of Virginia, Charlottesville, VA, USA
- https://ror.org/0153tk833 Center for Public Health Genomics, University of Virginia, Charlottesville, VA, USA
| | - Jiansheng Huang
- Novo Nordisk Research Center China, Novo Nordisk A/S, Beijing, China
| | - Yong Li
- Novo Nordisk Research Center China, Novo Nordisk A/S, Beijing, China
| | - Lijiang Ma
- https://ror.org/04a9tmd77 Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Dhanush Banka
- https://ror.org/0153tk833 Department of Biomedical Engineering, University of Virginia, Charlottesville, VA, USA
| | - Martin Wabitsch
- Division of Paediatric Endocrinology and Diabetes, Department of Paediatrics and Adolescent Medicine, Ulm University Medical Centre, Ulm, Germany
| | - Tianfang Wang
- Novo Nordisk Research Center China, Novo Nordisk A/S, Beijing, China
| | - Wen Ding
- Novo Nordisk Research Center China, Novo Nordisk A/S, Beijing, China
| | - Johan Lm Björkegren
- https://ror.org/04a9tmd77 Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Medicine, Karolinska Institutet, Huddinge, Stockholm, Sweden
| | - Mete Civelek
- https://ror.org/0153tk833 Department of Biomedical Engineering, University of Virginia, Charlottesville, VA, USA
- https://ror.org/0153tk833 Center for Public Health Genomics, University of Virginia, Charlottesville, VA, USA
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Ciarelli J, Thangaraj SV, Sun H, Domke S, Alkhatib B, Vyas AK, Gregg B, Sargis RM, Padmanabhan V. Developmental programming: An exploratory analysis of pancreatic islet compromise in female sheep resulting from gestational BPA exposure. Mol Cell Endocrinol 2024; 588:112202. [PMID: 38552943 DOI: 10.1016/j.mce.2024.112202] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Revised: 03/11/2024] [Accepted: 03/12/2024] [Indexed: 04/11/2024]
Abstract
Developmental exposure to endocrine disruptors like bisphenol A (BPA) are implicated in later-life metabolic dysfunction. Leveraging a unique sheep model of developmental programming, we conducted an exploratory analysis of the programming effects of BPA on the endocrine pancreas. Pregnant ewes were administered environmentally relevant doses of BPA during gestational days (GD) 30-90, and pancreata from female fetuses and adult offspring were analyzed. Prenatal BPA exposure induced a trend toward decreased islet insulin staining and β-cell count, increased glucagon staining and α-cell count, and increased α-cell/β-cell ratio. Findings were most consistent in fetal pancreata assessed at GD90 and in adult offspring exposed to the lowest BPA dose. While not assessed in fetuses, adult islet fibrosis was increased. Collectively, these data provide further evidence that early-life BPA exposure is a likely threat to human metabolic health. Future studies should corroborate these findings and decipher the molecular mechanisms of BPA's developmental endocrine toxicity.
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Affiliation(s)
- Joseph Ciarelli
- Department of Pediatrics, University of Michigan, Ann Arbor, MI, USA
| | | | - Haijing Sun
- Department of Epidemiology, University of Michigan, Ann Arbor, MI, USA
| | - Stephanie Domke
- Department of Pediatrics, University of Michigan, Ann Arbor, MI, USA
| | - Bashar Alkhatib
- Department of Pediatrics, Washington University, St. Louis, USA
| | | | - Brigid Gregg
- Department of Pediatrics, University of Michigan, Ann Arbor, MI, USA
| | - Robert M Sargis
- Department of Medicine, University of Illinois at Chicago, Chicago, IL, USA; Department of Medicine, Jesse Brown VA Medical Center, Chicago, IL, USA
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Zamora Z, Wang S, Chen YW, Diamante G, Yang X. Systematic transcriptome-wide meta-analysis across endocrine disrupting chemicals reveals shared and unique liver pathways, gene networks, and disease associations. ENVIRONMENT INTERNATIONAL 2024; 183:108339. [PMID: 38043319 PMCID: PMC11216742 DOI: 10.1016/j.envint.2023.108339] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Revised: 11/03/2023] [Accepted: 11/19/2023] [Indexed: 12/05/2023]
Abstract
Cardiometabolic disorders (CMD) are a growing public health problem across the world. Among the known cardiometabolic risk factors are compounds that induce endocrine and metabolic dysfunctions, such as endocrine disrupting chemicals (EDCs). To date, how EDCs influence molecular programs and cardiometabolic risks has yet to be fully elucidated, especially considering the complexity contributed by species-, chemical-, and dose-specific effects. Moreover, different experimental and analytical methodologies employed by different studies pose challenges when comparing findings across studies. To explore the molecular mechanisms of EDCs in a systematic manner, we established a data-driven computational approach to meta-analyze 30 human, mouse, and rat liver transcriptomic datasets for 4 EDCs, namely bisphenol A (BPA), bis(2-ethylhexyl) phthalate (DEHP), tributyltin (TBT), and perfluorooctanoic acid (PFOA). Our computational pipeline uniformly re-analyzed pre-processed quality-controlled microarray data and raw RNAseq data, derived differentially expressed genes (DEGs) and biological pathways, modeled gene regulatory networks and regulators, and determined CMD associations based on gene overlap analysis. Our approach revealed that DEHP and PFOA shared stable transcriptomic signatures that are enriched for genes associated with CMDs, suggesting similar mechanisms of action such as perturbations of peroxisome proliferator-activated receptor gamma (PPARγ) signaling and liver gene network regulators VNN1 and ACOT2. In contrast, TBT exhibited highly divergent gene signatures, pathways, network regulators, and disease associations from the other EDCs. In addition, we found that the rat, mouse, and human BPA studies showed highly variable transcriptomic patterns, providing molecular support for the variability in BPA responses. Our work offers insights into the commonality and differences in the molecular mechanisms of various EDCs and establishes a streamlined data-driven workflow to compare molecular mechanisms of environmental substances to elucidate the underlying connections between chemical exposure and disease risks.
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Affiliation(s)
- Zacary Zamora
- Molecular Toxicology Interdepartmental Program, University of California, Los Angeles (UCLA), Los Angeles, CA 90095, USA; Department of Integrative Biology and Physiology, University of California, Los Angeles (UCLA), Los Angeles, CA 90095, USA
| | - Susanna Wang
- Department of Integrative Biology and Physiology, University of California, Los Angeles (UCLA), Los Angeles, CA 90095, USA
| | - Yen-Wei Chen
- Molecular Toxicology Interdepartmental Program, University of California, Los Angeles (UCLA), Los Angeles, CA 90095, USA; Department of Integrative Biology and Physiology, University of California, Los Angeles (UCLA), Los Angeles, CA 90095, USA
| | - Graciel Diamante
- Department of Integrative Biology and Physiology, University of California, Los Angeles (UCLA), Los Angeles, CA 90095, USA.
| | - Xia Yang
- Molecular Toxicology Interdepartmental Program, University of California, Los Angeles (UCLA), Los Angeles, CA 90095, USA; Department of Integrative Biology and Physiology, University of California, Los Angeles (UCLA), Los Angeles, CA 90095, USA; Institute for Quantitative and Computational Biosciences, University of California, Los Angeles (UCLA), Los Angeles, CA 90095, USA.
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Lu H, Wang S, Zheng J, Zhu Y, Wang Y, Li H, Ge RS. Distinct inhibitory strength of bisphenol A analogues on human and rat 11β-hydroxysteroid dehydrogenase 1: 3D quantitative structure-activity relationship and in silico molecular docking analysis. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2023; 267:115638. [PMID: 37918333 DOI: 10.1016/j.ecoenv.2023.115638] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Revised: 10/07/2023] [Accepted: 10/25/2023] [Indexed: 11/04/2023]
Abstract
Bisphenol A (BPA) analogues are developed to replace BPA usage. However, their effects on 11β-hydroxysteroid dehydrogenase 1 (11β-HSD1) are largely unknown. The inhibitory effects of BPA and 10 BPA analogues with the substituents on the bridge moiety on human and rat 11β-HSD1 were explored in human and rat liver microsomes. The strength of inhibiting human 11β-HSD1 was bisphenol FL (IC50, 3.87 μM) > bisphenol Z (6.86 μM) > bisphenol AF (9.42 μM) > bisphenol C (16.14 μM) > bisphenol AP (32.14 μM) = bisphenol B (32.34 μM) > 4,4'-thiodiphenol (67.35 μM) > BPA (297.35 μM) > other BPA analogues (ineffective at 100 μM). The strength of inhibiting rat 11β-HSD1 was bisphenol Z (IC50, 14.44 μM) > 4,4'-thiodiphenol (19.01 μM) > bisphenol B (20.13 μM) > bisphenol F (22.10 μM) > bisphenol E (33.04 μM) > bisphenol AF (49.67 μM) > bisphenol C > (56.97 μM) > bisphenol AP (62.71 μM) >bisphenol FL (96.31 μM) > other BPA analogues (ineffective at 100 μM). Bisphenol A, AF, AP, B, C, F, FL, Z, and 4,4'-thiodiphenol bind to the active sites of human and rat 11β-HSD1. Regression of LogP and molecular weight with IC50 values revealed distinct inhibitory pattern (negative correlation for human 11β-HSD1 vs. positive correlation for rat enzyme). Regression of the lowest binding energy with IC50 values revealed a significant positive regression. 3D QSAR pharmacophore analysis showed one hydrogen bond acceptor and two hydrogen bond donors for human 11β-HSD1. In conclusion, most BPA analogues are more potent inhibitors of human and rat 11β-HSD1 enzymes and there is structure-dependent and species-dependent inhibition.
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Affiliation(s)
- Han Lu
- Department of Obstetrics and Gynecology, the Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, Zhejiang 325027, China; Department of Anesthesiology and Perioperative Medicine, the Second Affiliated Hospital and Yuying Children's Hospital, Wenzhou, Zhejiang 325027, China; Key Laboratory of Pediatric Anesthesiology, Ministry of Education, Wenzhou, Zhejiang 325027, China; Key Laboratory of Anesthesiology of Zhejiang Province, Wenzhou Medical University, Wenzhou, Zhejiang 325027, China; Key Laboratory of Environment and Male Reproductive Medicine of Wenzhou, Key Laboratory of Structural Malformations in Children of Zhejiang Province, Zhejiang Province, China
| | - Shaowei Wang
- Department of Obstetrics and Gynecology, the Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, Zhejiang 325027, China
| | - Jingyi Zheng
- Department of Obstetrics and Gynecology, the Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, Zhejiang 325027, China
| | - Yang Zhu
- Department of Obstetrics and Gynecology, the Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, Zhejiang 325027, China
| | - Yiyan Wang
- Department of Obstetrics and Gynecology, the Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, Zhejiang 325027, China
| | - Huitao Li
- Department of Obstetrics and Gynecology, the Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, Zhejiang 325027, China; Department of Anesthesiology and Perioperative Medicine, the Second Affiliated Hospital and Yuying Children's Hospital, Wenzhou, Zhejiang 325027, China; Key Laboratory of Pediatric Anesthesiology, Ministry of Education, Wenzhou, Zhejiang 325027, China; Key Laboratory of Anesthesiology of Zhejiang Province, Wenzhou Medical University, Wenzhou, Zhejiang 325027, China
| | - Ren-Shan Ge
- Department of Obstetrics and Gynecology, the Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, Zhejiang 325027, China; Department of Anesthesiology and Perioperative Medicine, the Second Affiliated Hospital and Yuying Children's Hospital, Wenzhou, Zhejiang 325027, China; Key Laboratory of Pediatric Anesthesiology, Ministry of Education, Wenzhou, Zhejiang 325027, China; Key Laboratory of Anesthesiology of Zhejiang Province, Wenzhou Medical University, Wenzhou, Zhejiang 325027, China; Key Laboratory of Environment and Male Reproductive Medicine of Wenzhou, Key Laboratory of Structural Malformations in Children of Zhejiang Province, Zhejiang Province, China.
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Reed JN, Huang J, Li Y, Ma L, Banka D, Wabitsch M, Wang T, Ding W, Björkegren JLM, Civelek M. Systems genetics analysis of human body fat distribution genes identifies Wnt signaling and mitochondrial activity in adipocytes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.06.556534. [PMID: 37732278 PMCID: PMC10508754 DOI: 10.1101/2023.09.06.556534] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/22/2023]
Abstract
BACKGROUND Excess fat in the abdomen is a sexually dimorphic risk factor for cardio-metabolic disease. The relative storage between abdominal and lower-body subcutaneous adipose tissue depots is approximated by the waist-to-hip ratio adjusted for body mass index (WHRadjBMI). Genome-wide association studies (GWAS) identified 346 loci near 495 genes associated with WHRadjBMI. Most of these genes have unknown roles in fat distribution, but many are expressed and putatively act in adipose tissue. We aimed to identify novel sex- and depot-specific drivers of WHRadjBMI using a systems genetics approach. METHODS We used two independent cohorts of adipose tissue gene expression with 362 - 444 males and 147 - 219 females, primarily of European ancestry. We constructed sex- and depot- specific Bayesian networks to model the gene-gene interactions from 8,492 adipose tissue genes. Key driver analysis identified genes that, in silico and putatively in vitro, regulate many others, including the 495 WHRadjBMI GWAS genes. Key driver gene function was determined by perturbing their expression in human subcutaneous pre-adipocytes using lenti-virus or siRNA. RESULTS 51 - 119 key drivers in each network were replicated in both cohorts. We used single-cell expression data to select replicated key drivers expressed in adipocyte precursors and mature adipocytes, prioritized genes which have not been previously studied in adipose tissue, and used public human and mouse data to nominate 53 novel key driver genes (10 - 21 from each network) that may regulate fat distribution by altering adipocyte function. In other cell types, 23 of these genes are found in crucial adipocyte pathways: Wnt signaling or mitochondrial function. We selected seven genes whose expression is highly correlated with WHRadjBMI to further study their effects on adipogenesis/Wnt signaling (ANAPC2, PSME3, RSPO1, TYRO3) or mitochondrial function (C1QTNF3, MIGA1, PSME3, UBR1).Adipogenesis was inhibited in cells overexpressing ANAPC2 and RSPO1 compared to controls. RSPO1 results are consistent with a positive correlation between gene expression in the subcutaneous depot and WHRadjBMI, therefore lower relative storage in the subcutaneous depot. RSPO1 inhibited adipogenesis by increasing β-catenin activation and Wnt-related transcription, thus repressing PPARG and CEBPA. PSME3 overexpression led to more adipogenesis than controls. In differentiated adipocytes, MIGA1 and UBR1 downregulation led to mitochondrial dysfunction, with lower oxygen consumption than controls; MIGA1 knockdown also lowered UCP1 expression. SUMMARY ANAPC2, MIGA1, PSME3, RSPO1, and UBR1 affect adipocyte function and may drive body fat distribution.
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Lu L, Shen L, Cui S, Huang Y, Gao Y, Zhu X, Lu S, Zhang C, Zhuang S. Angiogenic Activity and Mechanism for Bisphenols on Endothelial Cell and Mouse: Evidence of a Structural-Selective Effect. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2023; 57:11803-11813. [PMID: 37505069 DOI: 10.1021/acs.est.3c03883] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
Increased epidemiological evidence indicates the association of bisphenol exposure with human vascular disorders, while the underlying mechanism has not been clarified. Here, we sought to unveil the potential angiogenic effect and the underlying mechanism of bisphenols with different structural features using endothelial cells treated with an environmentally relevant concentration of bisphenols (range: 1 nM to 10 μM) and a C57BL/6 mouse model fed with doses of 0.002, 0.02, 2, and 20 mg/kg BW/day for 5 weeks. Bisphenol A (BPA) and bisphenol S (BPS) at a 1 nM level significantly increased tube formation by 45.1 and 30.2% and induced the microvessel sprouting, while tube length and microvessel sprouting were significantly inhibited by 37.2 and 55.7% after exposure to tetrabromobisphenol S (TBBPS) at 1 μM, respectively. Mechanistically, TBBPA and TBBPS significantly inhibited the interaction between phosphatidylinositol 3-kinase (PI3K) and thyroid receptor (TR), while BPA and BPS favored the interaction between PI3K and estrogen receptor (ER), resulting in abnormal PI3K signaling with consequent distinct angiogenic activity. BPA- and BPS-induced pro-angiogenic effects and TBBPS showed anti-angiogenic effects due to their distinct disruption on the TR/ER-PI3K pathway. Our work provided new evidence and mechanistic insight on the angiogenic activity of bisphenols and expanded the scope of endocrine disruptors with interference in vascular homeostasis.
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Affiliation(s)
- Liping Lu
- Key Laboratory of Environment Remediation and Ecological Health, Ministry of Education, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
- School of Public Health, Hangzhou Normal University, Hangzhou, Zhejiang 311121, China
| | - Lilai Shen
- Key Laboratory of Environment Remediation and Ecological Health, Ministry of Education, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Shixuan Cui
- Key Laboratory of Environment Remediation and Ecological Health, Ministry of Education, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Yizhou Huang
- Department of Gynecology, Women's Hospital, Zhejiang University School of Medicine, Hangzhou 310006, Zhejiang, China
| | - Yuchen Gao
- Key Laboratory of Environment Remediation and Ecological Health, Ministry of Education, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Xiaoming Zhu
- Department of Gynecology, Women's Hospital, Zhejiang University School of Medicine, Hangzhou 310006, Zhejiang, China
| | - Shaoyong Lu
- Department of Pathophysiology, School of Medicine, Shanghai Jiao Tong University, Shanghai 200025, China
| | - Chunlong Zhang
- Department of Environmental Sciences, University of Houston-Clear Lake, 2700 Bay Area Blvd., Houston, Texas 77058, United States
| | - Shulin Zhuang
- Key Laboratory of Environment Remediation and Ecological Health, Ministry of Education, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
- Department of Gynecology, Women's Hospital, Zhejiang University School of Medicine, Hangzhou 310006, Zhejiang, China
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Molina-López AM, Bujalance-Reyes F, Ayala-Soldado N, Mora-Medina R, Lora-Benítez A, Moyano-Salvago R. An Overview of the Health Effects of Bisphenol A from a One Health Perspective. Animals (Basel) 2023; 13:2439. [PMID: 37570248 PMCID: PMC10417040 DOI: 10.3390/ani13152439] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Revised: 07/26/2023] [Accepted: 07/27/2023] [Indexed: 08/13/2023] Open
Abstract
Bisphenol A (BPA) is a chemical compound, considered as an "emerging pollutant", that appears ubiquitously, contaminating the environment and food. It is an endocrine disruptor, found in a multitude of consumer products, as it is a constituent of polycarbonate used in the manufacture of plastics and epoxy resins. Many studies have evaluated the effects of BPA, using a wide range of doses and animal models. In this work, we carried out a review of relevant research related to the effects of BPA on health, through studies performed at different doses, in different animal models, and in human monitoring studies. Numerous effects of BPA on health have been described; in different animal species, it has been reported that it interferes with fertility in both females and males and causes alterations in their offspring, as well as being associated with an increase in hormone-dependent pathologies. Similarly, exposure to BPA has been related to other diseases of great relevance in public health such as obesity, hypertension, diabetes, or neurodevelopmental disorders. Its ubiquity and nonmonotonic behavior, triggering effects at exposure levels considered "safe", make it especially relevant when both animal and human populations are constantly and inadvertently exposed to this compound. Its effects at low exposure levels make it essential to establish safe exposure levels, and research into the effects of BPA must continue and be focused from a "One Health" perspective to take into account all the factors that could intervene in the development of a disease in any exposed organism.
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Affiliation(s)
- Ana M. Molina-López
- Departamento Anatomía y Anatomía Patológica Comparadas y Toxicología, Unidad de Investigación Competitiva Zoonosis y Enfermedades Emergentes desde la Perspectiva de Una Salud ENZOEM, Universidad de Córdoba, Campus de Rabanales, Edificio Darwin, E-14071 Córdoba, Spain;
| | - Francisca Bujalance-Reyes
- Departamento Anatomía y Anatomía Patológica Comparadas y Toxicología, Universidad de Córdoba, Campus de Rabanales, Edificio Darwin, E-14071 Córdoba, Spain; (F.B.-R.); (R.M.-M.); (A.L.-B.)
| | - Nahúm Ayala-Soldado
- Departamento Anatomía y Anatomía Patológica Comparadas y Toxicología, Universidad de Córdoba, Campus de Rabanales, Edificio Darwin, E-14071 Córdoba, Spain; (F.B.-R.); (R.M.-M.); (A.L.-B.)
| | - Rafael Mora-Medina
- Departamento Anatomía y Anatomía Patológica Comparadas y Toxicología, Universidad de Córdoba, Campus de Rabanales, Edificio Darwin, E-14071 Córdoba, Spain; (F.B.-R.); (R.M.-M.); (A.L.-B.)
| | - Antonio Lora-Benítez
- Departamento Anatomía y Anatomía Patológica Comparadas y Toxicología, Universidad de Córdoba, Campus de Rabanales, Edificio Darwin, E-14071 Córdoba, Spain; (F.B.-R.); (R.M.-M.); (A.L.-B.)
| | - Rosario Moyano-Salvago
- Departamento Anatomía y Anatomía Patológica Comparadas y Toxicología, Unidad de Investigación Competitiva Zoonosis y Enfermedades Emergentes desde la Perspectiva de Una Salud ENZOEM, Universidad de Córdoba, Campus de Rabanales, Edificio Darwin, E-14071 Córdoba, Spain;
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Abulehia H, Mohd Nor NS, Sheikh Abdul Kadir SH, Abdul Aziz M, Zulkifli S. The effects of trans fat diet intake on metabolic parameters and pancreatic tissue in offspring of prenatal bisphenol A exposed rats. Sci Rep 2023; 13:9322. [PMID: 37291156 PMCID: PMC10250527 DOI: 10.1038/s41598-023-36043-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Accepted: 05/28/2023] [Indexed: 06/10/2023] Open
Abstract
Bisphenol A (BPA) is a plasticiser used in the manufacturing of many products and its effects on human health remain controversial. Up till now, BPA involvement in metabolic syndrome risk and development is still not fully understood. In this study, we aimed to investigate the effect of prenatal BPA exposure with postnatal trans-fat diet intake on metabolic parameters and pancreatic tissue histology. Eighteen pregnant rats were divided into control (CTL), vehicle tween 80 (VHC), and BPA (5 mg/kg/day) from gestational day (GD) 2 until GD 21, then their weaning rat's offspring were fed with normal diet (ND) or trans-fat diet (TFD) from postnatal week (PNW) 3 until PNW 14. The rats were then sacrificed and the blood (biochemical analysis) and pancreatic tissues (histological analysis) were collected. Glucose, insulin, and lipid profile were measured. The study has shown that there was no significant difference between groups with regard to glucose, insulin, and lipid profiles (p > 0.05). All pancreatic tissues showed normal architecture with irregular islets of Langerhans in TFD intake groups compared to offspring that consumed ND. Furthermore, the pancreatic histomorphometry was also affected whereby the study findings revealed that there was a significant increase in the mean number of pancreatic islets in rats from BPA-TFD group (5.987 ± 0.3159 islets/field, p = 0.0022) compared to those fed with ND and BPA non-exposed. In addition, the results have found that prenatal BPA exposure resulted in a significant decrease in the pancreatic islets diameter of the BPA-ND group (183.3 ± 23.28 µm, p = 0.0022) compared to all other groups. In conclusion, prenatal BPA exposure with postnatal TFD in the offspring may affect glucose homeostasis and pancreatic islets in adulthood, and the effect may be more aggravated in late adulthood.
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Affiliation(s)
- Hala Abulehia
- Institute of Medical Molecular Biotechnology (IMMB), Faculty of Medicine, Universiti Teknologi MARA (UiTM), Cawangan Selangor, Kampus Sungai Buloh, Jalan Hospital, 47000, Sungai Buloh, Malaysia
| | - Noor Shafina Mohd Nor
- Institute of Medical Molecular Biotechnology (IMMB), Faculty of Medicine, Universiti Teknologi MARA (UiTM), Cawangan Selangor, Kampus Sungai Buloh, Jalan Hospital, 47000, Sungai Buloh, Malaysia.
- Department of Paediatrics, Faculty of Medicine, Universiti Teknologi MARA (UiTM), Cawangan Selangor, Kampus Sungai Buloh, Jalan Hospital, 47000, Sungai Buloh, Malaysia.
- Institute for Pathology, Laboratory and Forensic Medicine (I-PPerForM), Universiti Teknologi MARA (UiTM), Cawangan Selangor, Kampus Sungai Buloh, Jalan Hospital, 47000, Sungai Buloh, Malaysia.
| | - Siti Hamimah Sheikh Abdul Kadir
- Institute of Medical Molecular Biotechnology (IMMB), Faculty of Medicine, Universiti Teknologi MARA (UiTM), Cawangan Selangor, Kampus Sungai Buloh, Jalan Hospital, 47000, Sungai Buloh, Malaysia
- Institute for Pathology, Laboratory and Forensic Medicine (I-PPerForM), Universiti Teknologi MARA (UiTM), Cawangan Selangor, Kampus Sungai Buloh, Jalan Hospital, 47000, Sungai Buloh, Malaysia
- Department of Biochemistry and Molecular Medicine, Faculty of Medicine, Universiti Teknologi MARA (UiTM), Cawangan Selangor, Kampus Sungai Buloh, Jalan Hospital, 47000, Sungai Buloh, Malaysia
| | - Mardiana Abdul Aziz
- Department of Pathology, Faculty of Medicine, Universiti Teknologi MARA (UiTM), Cawangan Selangor, Kampus Sungai Buloh, Jalan Hospital, Sungai Buloh, 47000, Selangor, Malaysia
| | - Sarah Zulkifli
- Institute for Pathology, Laboratory and Forensic Medicine (I-PPerForM), Universiti Teknologi MARA (UiTM), Cawangan Selangor, Kampus Sungai Buloh, Jalan Hospital, 47000, Sungai Buloh, Malaysia
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McCabe CF, Goodrich JM, Bakulski KM, Domino SE, Jones TR, Colacino J, Dolinoy DC, Padmanabhan V. Probing prenatal bisphenol exposures and tissue-specific DNA methylation responses in cord blood, cord tissue, and placenta. Reprod Toxicol 2023; 115:74-84. [PMID: 36473650 PMCID: PMC9851062 DOI: 10.1016/j.reprotox.2022.11.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Revised: 11/15/2022] [Accepted: 11/21/2022] [Indexed: 12/12/2022]
Abstract
The early-gestational fetal epigenome establishes the landscape for fetal development and is susceptible to disruption via environmental stressors including chemical exposures. Research has explored how cell- and tissue-type-specific epigenomic signatures contribute to human disease, but how the epigenome in each tissue comparatively responds to environmental exposures is largely unknown. This pilot study compared DNA methylation in four previously identified genes across matched cord blood (CB), cord tissue (CT), and placental (PL) samples from 28 mother-infant pairs in tthe Michigan Mother Infant Pairs study; evaluated association between prenatal exposure to bisphenols (BPA, BPF, and BPS) and DNA methylation (DNAm) by tissue type; compared epigenome-wide DNAm of CB and PL; and explored associations between prenatal bisphenol exposures and epigenome-wide DNAm in PL. Bisphenol concentrations were quantified in first-trimester maternal urine. DNAm was assessed at four genes via pyrosequencing in three tissues; epigenome-wide DNAm analysis via Infinium MethylationEPIC array was completed on CB and PL. Candidate gene analysis revealed tissue-specific differences across all genes. In adjusted linear regression, BPA and BPF were associated with DNAm across candidate genes in PL but not CB and CT. Epigenome-wide comparison of matched CB and PL DNAm revealed tissue-specific differences at most CpG sites and modest associations between maternal first-trimester bisphenol exposures and PL but not CB DNAm. These data endorse inclusion of a variety of tissues in prenatal exposure studies. Overlapping and divergent responses in CB, CT, and PL demonstrate their utility in combination to capture a fuller picture of the epigenetic effect of developmental exposures.
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Affiliation(s)
- Carolyn F McCabe
- Department of Nutritional Sciences, University of Michigan School of Public Health, Ann Arbor, MI, USA
| | - Jaclyn M Goodrich
- Department of Environmental Health Sciences, University of Michigan School of Public Health, Ann Arbor, MI, USA
| | - Kelly M Bakulski
- Department of Epidemiology, University of Michigan School of Public Health, Ann Arbor, MI, USA
| | - Steven E Domino
- Department of Obstetrics and Gynecology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Tamara R Jones
- Department of Environmental Health Sciences, University of Michigan School of Public Health, Ann Arbor, MI, USA
| | - Justin Colacino
- Department of Environmental Health Sciences, University of Michigan School of Public Health, Ann Arbor, MI, USA
| | - Dana C Dolinoy
- Department of Nutritional Sciences, University of Michigan School of Public Health, Ann Arbor, MI, USA; Department of Environmental Health Sciences, University of Michigan School of Public Health, Ann Arbor, MI, USA
| | - Vasantha Padmanabhan
- Department of Environmental Health Sciences, University of Michigan School of Public Health, Ann Arbor, MI, USA; Department of Pediatrics, University of Michigan Medical School, Ann Arbor, MI, USA; Department of Obstetrics and Gynecology, University of Michigan Medical School, Ann Arbor, MI, USA.
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10
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Dabeer S, Raisuddin S. Perinatal exposure to environmental endocrine disruptor bisphenol A aggravates the onset of non-alcoholic fatty liver disease (NAFLD) in weanling F1 offspring of obese rats. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023; 30:3146-3165. [PMID: 35945320 DOI: 10.1007/s11356-022-22246-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/01/2022] [Accepted: 07/21/2022] [Indexed: 06/15/2023]
Abstract
Bisphenol A (BPA) is a major environmental pollutant and food contaminant with endocrine-disrupting effects on human and animal health. Perinatal and developmental exposure to BPA has been known to cause hepatotoxicity in adulthood. However, its intergenerational effects in a metabolically challenged population have been scarcely investigated. Our study was designed to assess the intergenerational effect of an environmentally relevant dose of BPA and diet-induced parental obesity on the hepatic health outcome of F1 offspring. Wistar rats were given a high-fat diet to induce obesity, followed by chronic low dosages of BPA (10 ppm × 180 days) in drinking water. Post-treatment, rats were crossed within groups to obtain the F1 generation. Weanling pups were observed for weight gain, levels of hepatic antioxidants, liver function enzymes, cholesterol, C-reactive protein, and triglyceride in the serum. Histological changes in the liver tissue were also investigated. mRNA expression of energy homeostasis genes (FTO and MCR-4) in the liver was analyzed alongside blood biomarkers. We observed higher birth weight and rapid weight gain in the test group in comparison with controls, which was consistent with the changes in mRNA and protein expression of FTO and MCR-4. BPA caused a significant, treatment-related change in the inflammatory marker C-reactive protein, lipid peroxidation, antioxidants, and lipid profile. These findings were accompanied by histological changes in the liver tissue characteristic of hepatic steatosis indicating the onset of the non-alcoholic fatty liver disease (NAFLD). Our study offers a link between exposure to BPA in parents and onset of NAFLD in their offspring.
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Affiliation(s)
- Sadaf Dabeer
- Molecular Toxicology Laboratory, Department of Medical Elementology and Toxicology, Jamia Hamdard (Hamdard University), New Delhi, 110062, India
- Currently at The Department of Exercise Science and Sport Management, WellStar College of Health and Human Services, Kennesaw State University, Kennesaw, GA, 30144, USA
- Currently at The Division of Endocrinology, Metabolism, and Lipids, School of Medicine, Emory University, Atlanta, GA, 30322, USA
| | - Sheikh Raisuddin
- Molecular Toxicology Laboratory, Department of Medical Elementology and Toxicology, Jamia Hamdard (Hamdard University), New Delhi, 110062, India.
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11
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Postnikova LA, Patkin EL. The possible effect of lactoferrin on the epigenetic characteristics of early mammalian embryos exposed to bisphenol A. Birth Defects Res 2022; 114:1199-1209. [PMID: 35451577 DOI: 10.1002/bdr2.2017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2021] [Revised: 03/15/2022] [Accepted: 03/30/2022] [Indexed: 11/05/2022]
Abstract
BACKGROUND The main objective of this review was to state a hypothetical mechanism of the antitoxic effect of lactoferrin (Lf) on embryos exposed to bisphenol A (BPA). On this basis, it is possible to suggest Lf as a potential protective health component before conception upon toxic effects and viral infections. METHODS The narrative review was performed using systematic review methods to identify relevant literature. The resources required for this study were obtained by searching the electronic database PubMed (MEDLINE). Articles were searched using the keywords "BPA," "lactoferrin," "DNA-methylation," "epigenetic," "mammals," "human," and "mouse." The inclusion criteria were as follows: (a) primary or original research; (b) study of epigenetic modification; and (c) study focuses on early mammalian development. RESULTS Presented data demonstrate that Lf can modulate epigenetical characteristic, such as DNA methylation and reactive oxygen species (ROS), and, thereby, may serve as a potential readily available pharmaceutical product. CONCLUSION Suggested hypothesis is based on the important interrelated role of changes in epigenetic modifications and oxidative stress in early embryogenesis under the influence of BPA and virus infection as a cause of the development of pathologies in the adult organism.
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Affiliation(s)
- Liubov A Postnikova
- Federal State Budget Scientific Institution "Institute of Experimental Medicine", St. Petersburg, Russia
| | - Eugene L Patkin
- Federal State Budget Scientific Institution "Institute of Experimental Medicine", St. Petersburg, Russia
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12
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Plante I, Winn LM, Vaillancourt C, Grigorova P, Parent L. Killing two birds with one stone: Pregnancy is a sensitive window for endocrine effects on both the mother and the fetus. ENVIRONMENTAL RESEARCH 2022; 205:112435. [PMID: 34843719 DOI: 10.1016/j.envres.2021.112435] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Revised: 11/22/2021] [Accepted: 11/23/2021] [Indexed: 06/13/2023]
Abstract
Pregnancy is a complex process requiring tremendous physiological changes in the mother in order to fulfill the needs of the growing fetus, and to give birth, expel the placenta and nurse the newborn. These physiological modifications are accompanied with psychological changes, as well as with variations in habits and behaviors. As a result, this period of life is considered as a sensitive window as impaired functional and physiological changes in the mother can have short- and long-term impacts on her health. In addition, dysregulation of the placenta and of mechanisms governing placentation have been linked to chronic diseases later-on in life for the fetus, in a concept known as the Developmental Origin of Health and Diseases (DOHaD). This concept stipulates that any change in the environment during the pre-conception and perinatal (in utero life and neonatal) period to puberty, can be "imprinted" in the organism, thereby impacting the health and risk of chronic diseases later in life. Pregnancy is a succession of events that is regulated, in large part, by hormones and growth factors. Therefore, small changes in hormonal balance can have important effects on both the mother and the developing fetus. An increasing number of studies demonstrate that exposure to endocrine disrupting compounds (EDCs) affect both the mother and the fetus giving rise to growing concerns surrounding these exposures. This review will give an overview of changes that happen during pregnancy with respect to the mother, the placenta, and the fetus, and of the current literature regarding the effects of EDCs during this specific sensitive window of exposure.
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Affiliation(s)
- Isabelle Plante
- INRS-Centre Armand-Frappier Santé Biotechnologie, Laval, QC, Canada.
| | - Louise M Winn
- Queen's University, School of Environmental Studies, Department of Biomedical and Molecular Sciences, Kingston, ON, Canada
| | | | - Petya Grigorova
- Département Science et Technologie, Université TELUQ, Montreal, QC, Canada
| | - Lise Parent
- Département Science et Technologie, Université TELUQ, Montreal, QC, Canada
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13
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Robitaille J, Denslow ND, Escher BI, Kurita-Oyamada HG, Marlatt V, Martyniuk CJ, Navarro-Martín L, Prosser R, Sanderson T, Yargeau V, Langlois VS. Towards regulation of Endocrine Disrupting chemicals (EDCs) in water resources using bioassays - A guide to developing a testing strategy. ENVIRONMENTAL RESEARCH 2022; 205:112483. [PMID: 34863984 DOI: 10.1016/j.envres.2021.112483] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 11/26/2021] [Accepted: 11/30/2021] [Indexed: 06/13/2023]
Abstract
Endocrine disrupting chemicals (EDCs) are found in every environmental medium and are chemically diverse. Their presence in water resources can negatively impact the health of both human and wildlife. Currently, there are no mandatory screening mandates or regulations for EDC levels in complex water samples globally. Bioassays, which allow quantifying in vivo or in vitro biological effects of chemicals are used commonly to assess acute toxicity in water. The existing OECD framework to identify single-compound EDCs offers a set of bioassays that are validated for the Estrogen-, Androgen-, and Thyroid hormones, and for Steroidogenesis pathways (EATS). In this review, we discussed bioassays that could be potentially used to screen EDCs in water resources, including in vivo and in vitro bioassays using invertebrates, fish, amphibians, and/or mammalians species. Strengths and weaknesses of samples preparation for complex water samples are discussed. We also review how to calculate the Effect-Based Trigger values, which could serve as thresholds to determine if a given water sample poses a risk based on existing quality standards. This work aims to assist governments and regulatory agencies in developing a testing strategy towards regulation of EDCs in water resources worldwide. The main recommendations include 1) opting for internationally validated cell reporter in vitro bioassays to reduce animal use & cost; 2) testing for cell viability (a critical parameter) when using in vitro bioassays; and 3) evaluating the recovery of the water sample preparation method selected. This review also highlights future research avenues for the EDC screening revolution (e.g., 3D tissue culture, transgenic animals, OMICs, and Adverse Outcome Pathways (AOPs)).
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Affiliation(s)
- Julie Robitaille
- Centre Eau Terre Environnement, Institut National de La Recherche Scientifique (INRS), Quebec City, QC, Canada
| | | | - Beate I Escher
- Helmholtz Centre for Environmental Research - UFZ, Leipzig, Germany; Eberhard Karls University Tübingen, Tübingen, Germany
| | | | - Vicki Marlatt
- Simon Fraser University, Burnaby, British Columbia, Canada
| | | | - Laia Navarro-Martín
- Institute of Environmental Assessment and Water Research (IDAEA-CSIC), Barcelona, Spain
| | | | - Thomas Sanderson
- Centre Armand-Frappier Santé Biotechnologie, INRS, Laval, QC, Canada
| | | | - Valerie S Langlois
- Centre Eau Terre Environnement, Institut National de La Recherche Scientifique (INRS), Quebec City, QC, Canada.
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14
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Ooi SK, Jiang H, Kang Y, Allard P. Examining the Developmental Trajectory of an in Vitro Model of Mouse Primordial Germ Cells following Exposure to Environmentally Relevant Bisphenol A Levels. ENVIRONMENTAL HEALTH PERSPECTIVES 2021; 129:97013. [PMID: 34585602 PMCID: PMC8480152 DOI: 10.1289/ehp8196] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Revised: 08/27/2021] [Accepted: 08/31/2021] [Indexed: 06/13/2023]
Abstract
BACKGROUND Animal-based studies indicate that bisphenol A (BPA) exposure is detrimental to reproductive health, but its impact on the earliest stages of germ cell development remains poorly defined. OBJECTIVES Using a murine in vitro model of early germ cell specification and differentiation, we sought to assess whether exposure to low levels of BPA prior to formation of primordial germ cells (PGCs) alters their differentiation trajectory and unique molecular program. METHODS We used an established method of in vitro differentiation of mouse embryonic stem cells (ESCs) into epiblast-like cells (EpiLCs) followed by PGC-like cells (PGCLCs), which together recapitulate defined stages of early germ cell development. Cellular consequences were determined using hemocytometer-based cell counting, fixation, and intracellular staining, followed by flow cytometry/fluorescence-activated cell sorting (FACS) of cells exposed to increasing concentrations (range: 1 nM-10 μM) of BPA. To interrogate and characterize gene expression differences resulting from BPA exposure, we also generated RNA-seq libraries from RNA extracted from FACS-purified PGCLCs and performed transcriptome analysis using bioinformatics-based approaches. RESULTS Exposure of EpiLCs to BPA resulted in higher numbers of cells that were associated with a higher proportion of cells in S-phase as well as a lower proportion undergoing apoptosis; this difference occurred in a concentration-dependent manner. Exposure also resulted in a greater fraction of EpiLCs showing signs of DNA damage. Remarkably, EpiLC exposure did not negatively affect PGC specification and resulted in a concentration-dependent effect on PGCLC proliferation in XX but not XY cells. PGCLC transcriptome analysis revealed an aberrant program with significant deregulation of X-linked genes and retrotransposon expression. Differential gene expression analysis also revealed the deregulation of genes associated with lipid metabolism as well as deregulated expression of genes associated with later stages of gametogenesis. CONCLUSIONS To the best of our knowledge our findings represent the first characterization of the consequences of early BPA exposure on a model of mammalian PGC development, highlighting altered cell behavior, altered underlying pathways, and altered molecular processes. https://doi.org/10.1289/EHP8196.
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Affiliation(s)
- Steen K.T. Ooi
- UCLA Institute for Society & Genetics, University of California, Los Angeles, Los Angeles, California, USA
| | - Hui Jiang
- UCLA Institute for Society & Genetics, University of California, Los Angeles, Los Angeles, California, USA
| | - Yanyuan Kang
- UCLA Institute for Society & Genetics, University of California, Los Angeles, Los Angeles, California, USA
| | - Patrick Allard
- UCLA Institute for Society & Genetics, University of California, Los Angeles, Los Angeles, California, USA
- Molecular Biology Institute, University of California, Los Angeles, Los Angeles, California, USA
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15
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Ding J, Blencowe M, Nghiem T, Ha SM, Chen YW, Li G, Yang X. Mergeomics 2.0: a web server for multi-omics data integration to elucidate disease networks and predict therapeutics. Nucleic Acids Res 2021; 49:W375-W387. [PMID: 34048577 PMCID: PMC8262738 DOI: 10.1093/nar/gkab405] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2021] [Revised: 04/28/2021] [Accepted: 05/02/2021] [Indexed: 12/13/2022] Open
Abstract
The Mergeomics web server is a flexible online tool for multi-omics data integration to derive biological pathways, networks, and key drivers important to disease pathogenesis and is based on the open source Mergeomics R package. The web server takes summary statistics of multi-omics disease association studies (GWAS, EWAS, TWAS, PWAS, etc.) as input and features four functions: Marker Dependency Filtering (MDF) to correct for known dependency between omics markers, Marker Set Enrichment Analysis (MSEA) to detect disease relevant biological processes, Meta-MSEA to examine the consistency of biological processes informed by various omics datasets, and Key Driver Analysis (KDA) to identify essential regulators of disease-associated pathways and networks. The web server has been extensively updated and streamlined in version 2.0 including an overhauled user interface, improved tutorials and results interpretation for each analytical step, inclusion of numerous disease GWAS, functional genomics datasets, and molecular networks to allow for comprehensive omics integrations, increased functionality to decrease user workload, and increased flexibility to cater to user-specific needs. Finally, we have incorporated our newly developed drug repositioning pipeline PharmOmics for prediction of potential drugs targeting disease processes that were identified by Mergeomics. Mergeomics is freely accessible at http://mergeomics.research.idre.ucla.edu and does not require login.
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Affiliation(s)
- Jessica Ding
- Department of Integrative Biology and Physiology, University of California, Los Angeles, 610 Charles E. Young Drive East, Los Angeles, CA 90095, USA
- Interdepartmental Program of Molecular, Cellular and Integrative Physiology, University of California, Los Angeles, 610 Charles E. Young Drive East, Los Angeles, CA 90095, USA
| | - Montgomery Blencowe
- Department of Integrative Biology and Physiology, University of California, Los Angeles, 610 Charles E. Young Drive East, Los Angeles, CA 90095, USA
- Interdepartmental Program of Molecular, Cellular and Integrative Physiology, University of California, Los Angeles, 610 Charles E. Young Drive East, Los Angeles, CA 90095, USA
| | - Thien Nghiem
- Department of Integrative Biology and Physiology, University of California, Los Angeles, 610 Charles E. Young Drive East, Los Angeles, CA 90095, USA
| | - Sung-min Ha
- Department of Integrative Biology and Physiology, University of California, Los Angeles, 610 Charles E. Young Drive East, Los Angeles, CA 90095, USA
| | - Yen-Wei Chen
- Department of Integrative Biology and Physiology, University of California, Los Angeles, 610 Charles E. Young Drive East, Los Angeles, CA 90095, USA
- Interdepartmental Program of Molecular Toxicology, University of California, Los Angeles, 610 Charles E. Young Drive East, Los Angeles, CA 90095, USA
| | - Gaoyan Li
- Department of Integrative Biology and Physiology, University of California, Los Angeles, 610 Charles E. Young Drive East, Los Angeles, CA 90095, USA
- Interdepartmental Program of Molecular, Cellular and Integrative Physiology, University of California, Los Angeles, 610 Charles E. Young Drive East, Los Angeles, CA 90095, USA
| | - Xia Yang
- Department of Integrative Biology and Physiology, University of California, Los Angeles, 610 Charles E. Young Drive East, Los Angeles, CA 90095, USA
- Interdepartmental Program of Molecular, Cellular and Integrative Physiology, University of California, Los Angeles, 610 Charles E. Young Drive East, Los Angeles, CA 90095, USA
- Interdepartmental Program of Molecular Toxicology, University of California, Los Angeles, 610 Charles E. Young Drive East, Los Angeles, CA 90095, USA
- Interdepartmental Program of Bioinformatics, University of California, Los Angeles, 610 Charles E. Young Drive East, Los Angeles, CA 90095, USA
- Institute for Quantitative and Computational Biosciences, University of California, Los Angeles, 610 Charles E. Young Drive East, Los Angeles, CA 90095, USA
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16
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Shih MK, Tain YL, Chen YW, Hsu WH, Yeh YT, Chang SKC, Liao JX, Hou CY. Resveratrol Butyrate Esters Inhibit Obesity Caused by Perinatal Exposure to Bisphenol A in Female Offspring Rats. Molecules 2021; 26:molecules26134010. [PMID: 34209270 PMCID: PMC8271435 DOI: 10.3390/molecules26134010] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Revised: 06/17/2021] [Accepted: 06/28/2021] [Indexed: 01/13/2023] Open
Abstract
Resveratrol butyrate esters (RBE) are derivatives of resveratrol (RSV) and butyric acid and exhibit biological activity similar to that of RSV but with higher bioavailability. The aim of this study was designed as an animal experiment to explore the effects of RBE on the serum biochemistry, and fat deposits in the offspring rats exposed to bisphenol A (BPA), along with the growth and decline of gut microbiota. We constructed an animal model of perinatal Bisphenol A (BPA) exposure to observe the effects of RBE supplementation on obesity, blood lipids, and intestinal microbiota in female offspring rats. Perinatal exposure to BPA led to weight gain, lipid accumulation, high levels of blood lipids, and deterioration of intestinal microbiota in female offspring rats. RBE supplementation reduced the weight gain and lipid accumulation caused by BPA, optimised the levels of blood lipids, significantly reduced the Firmicutes/Bacteroidetes (F/B) ratio, and increased and decreased the abundance of S24-7 and Lactobacillus, respectively. The analysis of faecal short-chain fatty acid (SCFA) levels revealed that BPA exposure increased the faecal concentration of acetate, which could be reduced via RBE supplementation. However, the faecal concentrations of propionate and butyrate were not only significantly lower than that of acetate, but also did not significantly change in response to BPA exposure or RBE supplementation. Hence, RBE can suppress BPA-induced obesity in female offspring rats, and it demonstrates excellent modulatory activity on intestinal microbiota, with potential applications in perinatological research.
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Affiliation(s)
- Ming-Kuei Shih
- Graduate Institute of Food Culture and Innovation, National Kaohsiung University of Hospitality and Tourism, No.1, Songhe Rd., Xiaogang Dist., Kaohsiung City 812, Taiwan;
| | - You-Lin Tain
- Department of Pediatrics, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung 833, Taiwan;
- Institute for Translational Research in Biomedicine, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung 833, Taiwan
| | - Yu-Wei Chen
- Department of Medicine, Chang Gung University, Linkow 333, Taiwan;
| | - Wei-Hsuan Hsu
- Department of Food Safety/Hygiene and Risk Management, College of Medicine, National Cheng Kung University, Tainan 704, Taiwan;
| | - Yao-Tsung Yeh
- Aging and Disease Prevention Research Center, Fooyin University, Kaohsiung 831, Taiwan;
- Biomed Analysis Center, Fooyin University Hospital, Pingtung 928, Taiwan
| | - Sam K. C. Chang
- Experimental Seafood Processing Laboratory, Costal Research and Extension Center, Mississippi State University, Starkville, MS 39567, USA;
- Department of Food Science, Nutrition and Health Promotion, Mississippi State University, Starkville, MS 39762, USA
| | - Jin-Xian Liao
- Department of Seafood Science, National Kaohsiung University of Science and Technology, Kaohsiung 824, Taiwan;
| | - Chih-Yao Hou
- Department of Seafood Science, National Kaohsiung University of Science and Technology, Kaohsiung 824, Taiwan;
- Correspondence: ; Tel.: +886-985300345; Fax: +886-7-3640364
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17
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Streifer M, Gore AC. Epigenetics, estrogenic endocrine-disrupting chemicals (EDCs), and the brain. ENDOCRINE-DISRUPTING CHEMICALS 2021; 92:73-99. [DOI: 10.1016/bs.apha.2021.03.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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18
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Diamante G, Cely I, Zamora Z, Ding J, Blencowe M, Lang J, Bline A, Singh M, Lusis AJ, Yang X. Systems toxicogenomics of prenatal low-dose BPA exposure on liver metabolic pathways, gut microbiota, and metabolic health in mice. ENVIRONMENT INTERNATIONAL 2021; 146:106260. [PMID: 33221593 PMCID: PMC7775895 DOI: 10.1016/j.envint.2020.106260] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Revised: 10/30/2020] [Accepted: 10/31/2020] [Indexed: 05/06/2023]
Abstract
Bisphenol A (BPA) is an industrial plasticizer widely found in consumer products, and exposure to BPA during early development has been associated with the prevalence of various cardiometabolic diseases including obesity, metabolic syndrome, type 2 diabetes, and cardiovascular diseases. To elucidate the molecular perturbations underlying the connection of low-dose prenatal BPA exposure to cardiometabolic diseases, we conducted a multi-dimensional systems biology study assessing the liver transcriptome, gut microbial community, and diverse metabolic phenotypes in both male and female mouse offspring exposed to 5 μg/kg/day BPA during gestation. Prenatal exposure to low-dose BPA not only significantly affected liver genes involved in oxidative phosphorylation, PPAR signaling and fatty acid metabolism, but also affected the gut microbial composition in an age- and sex-dependent manner. Bacteria such as those belonging to the S24-7 and Lachnospiraceae families were correlated with offspring phenotypes, differentially expressed liver metabolic genes such as Acadl and Dgat1, and key drivers identified in our gene network modeling such as Malat1 and Apoa2. This multiomics study provides insight into the relationship between gut bacteria and host liver genes that could contribute to cardiometabolic disease risks upon low-dose BPA exposure.
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Affiliation(s)
- Graciel Diamante
- Department of Integrative Biology and Physiology, University of California, Los Angeles (UCLA), Los Angeles, CA 90095, USA; Molecular Toxicology Interdepartmental Program, University of California, Los Angeles (UCLA), Los Angeles, CA 90095, USA
| | - Ingrid Cely
- Department of Integrative Biology and Physiology, University of California, Los Angeles (UCLA), Los Angeles, CA 90095, USA
| | - Zacary Zamora
- Department of Integrative Biology and Physiology, University of California, Los Angeles (UCLA), Los Angeles, CA 90095, USA
| | - Jessica Ding
- Department of Integrative Biology and Physiology, University of California, Los Angeles (UCLA), Los Angeles, CA 90095, USA; Interdepartmental Program of Molecular, Cellular and Integrative Physiology, University of California, Los Angeles (UCLA), Los Angeles, CA 90095, USA
| | - Montgomery Blencowe
- Department of Integrative Biology and Physiology, University of California, Los Angeles (UCLA), Los Angeles, CA 90095, USA; Interdepartmental Program of Molecular, Cellular and Integrative Physiology, University of California, Los Angeles (UCLA), Los Angeles, CA 90095, USA
| | - Jennifer Lang
- Department of Medicine/Division of Cardiology, University of California, Los Angeles, CA (UCLA), Los Angeles, CA 90095, USA
| | - Abigail Bline
- Molecular Toxicology Interdepartmental Program, University of California, Los Angeles (UCLA), Los Angeles, CA 90095, USA
| | - Maya Singh
- Department of Integrative Biology and Physiology, University of California, Los Angeles (UCLA), Los Angeles, CA 90095, USA
| | - Aldons J Lusis
- Department of Medicine/Division of Cardiology, University of California, Los Angeles, CA (UCLA), Los Angeles, CA 90095, USA; Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles (UCLA), Los Angeles, CA 90095, USA
| | - Xia Yang
- Department of Integrative Biology and Physiology, University of California, Los Angeles (UCLA), Los Angeles, CA 90095, USA; Molecular Toxicology Interdepartmental Program, University of California, Los Angeles (UCLA), Los Angeles, CA 90095, USA; Institute for Quantitative and Computational Biosciences, University of California, Los Angeles (UCLA), Los Angeles, CA 90095, USA.
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19
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Zhang G, Meng Q, Blencowe M, Agrawal R, Gomez-Pinilla F, Yang X. Multi-Tissue Multi-Omics Nutrigenomics Indicates Context-Specific Effects of Docosahexaenoic Acid on Rat Brain. Mol Nutr Food Res 2020; 64:e2000788. [PMID: 33063454 PMCID: PMC8046846 DOI: 10.1002/mnfr.202000788] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2020] [Revised: 10/07/2020] [Indexed: 11/09/2022]
Abstract
SCOPE The influence of docosahexaenoic acid (DHA) on cardiometabolic and cognitive phenotypes, and multi-omic alterations in the brain under two metabolic conditions is explored to understand context-specific nutritional effects. METHODS AND RESULTS Rats are randomly assigned to a DHA-rich or a control chow diet while drinking water or high fructose solution, followed by profiling of metabolic and cognitive phenotypes and the transcriptome and DNA methylome of the hypothalamus and hippocampus. DHA reduces serum triglyceride and improves insulin resistance and memory exclusively in the fructose-consuming rats. In hippocampus, DHA affects genes related to synapse functions in the chow group but immune functions in the fructose group; in hypothalamus, DHA alters immune pathways in the chow group but metabolic pathways in the fructose group. Network modeling reveals context-specific regulators of DHA effects, including Klf4 and Dusp1 for chow condition and Lum, Fn1, and Col1a1 for fructose condition in hippocampus, as well as Cyr61, JunB, Ier2, and Pitx2 under chow condition and Hcar1, Cdh1, and Osr1 under fructose condition in hypothalamus. CONCLUSION DHA exhibits differential influence on epigenetic loci, genes, pathways, and metabolic and cognitive phenotypes under different dietary contexts, supporting population stratification in DHA studies to achieve precision nutrition.
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Affiliation(s)
- Guanglin Zhang
- Department of Integrative Biology and Physiology, University of California, Los Angeles, 610 Charles E. Young Drive East, Los Angeles, CA 90095, USA
- Department of Neurosurgery, University of California, Los Angeles, Los Angeles, CA, 90095, USA
| | - Qingying Meng
- Department of Integrative Biology and Physiology, University of California, Los Angeles, 610 Charles E. Young Drive East, Los Angeles, CA 90095, USA
| | - Montgomery Blencowe
- Department of Integrative Biology and Physiology, University of California, Los Angeles, 610 Charles E. Young Drive East, Los Angeles, CA 90095, USA
- Molecular, Cellular, and Integrative Physiology Interdepartmental Program, University of California, Los Angeles, 610 Charles E. Young Drive East, Los Angeles, CA 90095, USA
| | - Rahul Agrawal
- Department of Integrative Biology and Physiology, University of California, Los Angeles, 610 Charles E. Young Drive East, Los Angeles, CA 90095, USA
- Department of Neurosurgery, University of California, Los Angeles, Los Angeles, CA, 90095, USA
- Brain Injury Research Center, University of California, Los Angeles, Los Angeles, CA, 90095, USA
| | - Fernando Gomez-Pinilla
- Department of Integrative Biology and Physiology, University of California, Los Angeles, 610 Charles E. Young Drive East, Los Angeles, CA 90095, USA
- Department of Neurosurgery, University of California, Los Angeles, Los Angeles, CA, 90095, USA
- Brain Injury Research Center, University of California, Los Angeles, Los Angeles, CA, 90095, USA
| | - Xia Yang
- Department of Integrative Biology and Physiology, University of California, Los Angeles, 610 Charles E. Young Drive East, Los Angeles, CA 90095, USA
- Molecular, Cellular, and Integrative Physiology Interdepartmental Program, University of California, Los Angeles, 610 Charles E. Young Drive East, Los Angeles, CA 90095, USA
- Institute for Quantitative and Computational Biosciences, University of California, Los Angeles, 610 Charles E. Young Drive East, Los Angeles, CA 90095, USA
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20
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Lucendo-Villarin B, Nell P, Hellwig B, Filis P, Feuerborn D, O'Shaughnessy PJ, Godoy P, Rahnenführer J, Hengstler JG, Cherianidou A, Sachinidis A, Fowler PA, Hay DC. Genome-wide expression changes induced by bisphenol A, F and S in human stem cell derived hepatocyte-like cells. EXCLI JOURNAL 2020; 19:1459-1476. [PMID: 33312107 PMCID: PMC7726493 DOI: 10.17179/excli2020-2934] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Accepted: 10/28/2020] [Indexed: 12/12/2022]
Abstract
The debate about possible adverse effects of bisphenol A (BPA) has been ongoing for decades. Bisphenol F (BPF) and S (BPS) have been suggested as “safer” alternatives. In the present study we used hepatocyte-like cells (HLCs) derived from the human embryonic stem cell lines Man12 and H9 to compare the three bisphenol derivatives. Stem cell-derived progenitors were produced using an established system and were exposed to BPA, BPF and BPS for 8 days during their transition to HLCs. Subsequently, we examined cell viability, inhibition of cytochrome P450 (CYP) activity, and genome-wide RNA profiles. Sub-cytotoxic, inhibitory concentrations (IC50) of CYP3A were 20, 9.5 and 25 µM for BPA, BPF and BPS in Man12 derived HLCs, respectively. The corresponding concentrations for H9-derived HLCs were 19, 29 and 31 µM. These IC50 concentrations were used to study global expression changes in this in vitro study and are higher than unconjugated BPA in serum of the general population. A large overlap of up- as well as downregulated genes induced by the three bisphenol derivatives was seen. This is at least 28-fold higher compared to randomly expected gene expression changes. Moreover, highly significant correlations of expression changes induced by the three bisphenol derivatives were obtained in pairwise comparisons. Dysregulated genes were associated with reduced metabolic function, cellular differentiation, embryonic development, cell survival and apoptosis. In conclusion, no major differences in cytochrome inhibitory activities of BPA, BPF and BPS were observed and gene expression changes showed a high degree of similarity.
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Affiliation(s)
- B Lucendo-Villarin
- Centre for Regenerative Medicine, University of Edinburgh, Edinburgh, UK
| | - P Nell
- IfADo-Leibniz Research Centre for Working Environment and Human Factors at the Technical University Dortmund, Dortmund, Germany
| | - B Hellwig
- Department of Statistics, Technical University Dortmund, Dortmund, Germany
| | - P Filis
- Institute of Medical Sciences, University of Aberdeen, Aberdeen, UK
| | - D Feuerborn
- IfADo-Leibniz Research Centre for Working Environment and Human Factors at the Technical University Dortmund, Dortmund, Germany
| | - P J O'Shaughnessy
- Institute of Biodiversity, Animal Health & Comparative Medicine, University of Glasgow, UK
| | - P Godoy
- IfADo-Leibniz Research Centre for Working Environment and Human Factors at the Technical University Dortmund, Dortmund, Germany
| | - J Rahnenführer
- Department of Statistics, Technical University Dortmund, Dortmund, Germany
| | - J G Hengstler
- IfADo-Leibniz Research Centre for Working Environment and Human Factors at the Technical University Dortmund, Dortmund, Germany
| | - A Cherianidou
- Institute of Neurophysiology and Center for Molecular Medicine Cologne (CMMC), University of Cologne (UKK), Cologne, Germany
| | - A Sachinidis
- Institute of Neurophysiology and Center for Molecular Medicine Cologne (CMMC), University of Cologne (UKK), Cologne, Germany
| | - P A Fowler
- Institute of Medical Sciences, University of Aberdeen, Aberdeen, UK
| | - D C Hay
- Centre for Regenerative Medicine, University of Edinburgh, Edinburgh, UK
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21
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Martínez R, Tu W, Eng T, Allaire-Leung M, Piña B, Navarro-Martín L, Mennigen JA. Acute and long-term metabolic consequences of early developmental Bisphenol A exposure in zebrafish (Danio rerio). CHEMOSPHERE 2020; 256:127080. [PMID: 32450349 DOI: 10.1016/j.chemosphere.2020.127080] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Revised: 05/12/2020] [Accepted: 05/13/2020] [Indexed: 05/22/2023]
Abstract
Bisphenol A (BPA) is an estrogenic contaminant linked to metabolic disruption. Developmental BPA exposure is of particular concern, as organizational effects may irreversibly disrupt metabolism at later life-stages. While BPA exposures in adult fish elicit metabolic perturbations similar to effects described in rodents, the metabolic effects of developmental BPA exposure in juvenile fish remain largely unknown. Following embryonic zebrafish exposure to BPA (0.1, 1 and 4 mg/L) and EE2 (10 ng/L) from 2 to 5 dpf, we assessed the metabolic phenotype in larvae (4-6 dpf) and juveniles (43-49 dpf) which had been divided into regular-fed and overfed groups at 29 dpf. Developmental BPA exposure in larvae dose-dependently reduced food-intake and locomotion and increased energy expenditure. Juveniles (29 dpf) exhibited a transient increase in body weight after developmental BPA exposure and persistent diet-dependent locomotion changes (43-49 dpf). At the molecular level, glucose and lipid metabolism-related transcript abundance clearly separated BPA exposed fish from controls and EE2 exposed fish at the larval stage, in juveniles on a regular diet and, to a lesser extent, in overfed juveniles. In general, the metabolic endpoints affected by BPA exposure were not mimicked by EE2 treatment. We conclude that developmental BPA exposure elicits acute metabolic effects in zebrafish larvae and fewer transient and persistent effects in juveniles and that these metabolic effects are largely independent of BPA's estrogenicity.
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Affiliation(s)
- Rubén Martínez
- Department of Environmental Chemistry, Institute of Environmental Assessment and Water Research, IDAEA-CSIC, Jordi Girona, Barcelona, Spain; Department of Cellular Biology, Physiology and Immunology, Universitat de Barcelona (UB), Barcelona, Spain
| | - Wenqing Tu
- Research Institute of Poyang Lake, Jiangxi Academy of Sciences, Nanchang 330012, China
| | - Tyler Eng
- Department of Biology, University of Ottawa, 20 Marie-Curie K1N 6N5, Ottawa, Ontario, Canada
| | - Melissa Allaire-Leung
- Department of Biology, University of Ottawa, 20 Marie-Curie K1N 6N5, Ottawa, Ontario, Canada
| | - Benjamin Piña
- Department of Environmental Chemistry, Institute of Environmental Assessment and Water Research, IDAEA-CSIC, Jordi Girona, Barcelona, Spain
| | - Laia Navarro-Martín
- Department of Environmental Chemistry, Institute of Environmental Assessment and Water Research, IDAEA-CSIC, Jordi Girona, Barcelona, Spain
| | - Jan A Mennigen
- Department of Biology, University of Ottawa, 20 Marie-Curie K1N 6N5, Ottawa, Ontario, Canada.
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22
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Yang X. Multitissue Multiomics Systems Biology to Dissect Complex Diseases. Trends Mol Med 2020; 26:718-728. [PMID: 32439301 PMCID: PMC7395877 DOI: 10.1016/j.molmed.2020.04.006] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Revised: 04/18/2020] [Accepted: 04/26/2020] [Indexed: 12/20/2022]
Abstract
Most complex diseases involve genetic and environmental risk factors, engage multiple cells and tissues, and follow a polygenic or omnigenic model depicting numerous genes contributing to pathophysiology. These multidimensional complexities pose challenges to traditional approaches that examine individual factors. In turn, multitissue multiomics systems biology has emerged to comprehensively elucidate within- and cross-tissue molecular networks underlying gene-by-environment interactions and contributing to complex diseases. The power of systems biology in retrieving novel insights and formulating new hypotheses has been well documented. However, the field faces various challenges that call for debate and action. In this opinion article, I discuss the concepts, benefits, current state, and challenges of the field and point to the next steps toward network-based systems medicine.
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Affiliation(s)
- Xia Yang
- Department of Integrative Biology and Physiology, University of California, Los Angeles, CA, USA.
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Impact of Sex and Age on the Mevalonate Pathway in the Brain: A Focus on Effects Induced by Maternal Exposure to Exogenous Compounds. Metabolites 2020; 10:metabo10080304. [PMID: 32722471 PMCID: PMC7463490 DOI: 10.3390/metabo10080304] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Revised: 07/19/2020] [Accepted: 07/23/2020] [Indexed: 12/21/2022] Open
Abstract
The mevalonate pathway produces cholesterol and other compounds crucial for numerous cellular processes. It is well known that age and sex modulate this pathway in the liver. Recently, similar effects were also noted in different brain areas, suggesting that alterations of the mevalonate pathway are at the root of marked sex-specific disparities in some neurodevelopmental disorders related to disturbed cholesterol homeostasis. Here, we show how the mevalonate pathway is modulated in a sex-, age- and region-specific manner, and how maternal exposure to exogenous compounds can disturb the regulation of this pathway in the brain, possibly inducing functional alterations.
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24
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Aydemir I, Özbey C, Özkan O, Kum Ş, Tuğlu Mİ. Investigation of the effects of bisphenol-A exposure on lymphoid system in prenatal stage. Toxicol Ind Health 2020; 36:502-513. [PMID: 32696725 DOI: 10.1177/0748233720941759] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Bisphenol-A (BPA) used in the production of plastic materials is a temperature-soluble agent. It also has a steroid hormone-like activity; therefore, it poses a danger to human health. In our study, we aimed to investigate the effects of BPA on lymph node and spleen in male rats exposed to this agent during prenatal stage. The pregnant female rats were divided into four groups: control, sham, low dose (300 µg/kg BPA), and high dose (900 µg/kg BPA). BPA was dissolved in 1 mL of corn oil and administered to the pregnant rats every day during pregnancy. On the 21st and 45th day after the birth, male rats' lymph node and spleen samples were taken and histopathological examination was performed. Samples were stained with hematoxylin and eosin to determine the general histological appearance, and with CD3 and CD20 immunohistochemically. The results of staining were evaluated by H-score, and statistical analysis was performed. In the samples, BPA applications were not found to cause significant tissue damage. But there was a significant decrease in the immunoreactivities of CD3 and CD20 after BPA applications in both 21st and 45th day samples. After high dose BPA administration, decreased CD3 immunoreactivity was statistically significant. It is thought that BPA does not cause histologically significant tissue damage, but it may impair organ function at cellular level. The investigation of molecules involved in organ function will be useful in revealing the mechanisms that will cause dysfunction.
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Affiliation(s)
- Işil Aydemir
- Department of Histology and Embryology, Faculty of Medicine, Niğde Ömer Halisdemir University, Niğde, Turkey
| | - Caner Özbey
- Department of Pathology, Faculty of Medicine, Niğde Ömer Halisdemir University, Niğde, Turkey
| | - Oktay Özkan
- Department of Medicinal Pharmacology, Faculty of Medicine, Niğde Ömer Halisdemir University, Niğde, Turkey
| | - Şadiye Kum
- Department of Histology and Embryology, Faculty of Veterinary Medicine, Aydın Adnan Menderes University, Aydın, Turkey
| | - Mehmet İbrahim Tuğlu
- Department of Histology and Embryology, Faculty of Medicine, Manisa Celal Bayar University, Manisa, Turkey
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25
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Bisphenol a Exposure in Utero Disrupts Hypothalamic Gene Expression Particularly Genes Suspected in Autism Spectrum Disorders and Neuron and Hormone Signaling. Int J Mol Sci 2020; 21:ijms21093129. [PMID: 32365465 PMCID: PMC7246794 DOI: 10.3390/ijms21093129] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Revised: 04/23/2020] [Accepted: 04/27/2020] [Indexed: 01/09/2023] Open
Abstract
Bisphenol A (BPA) is an endocrine-disrupting compound detected in the urine of more than 92% of humans, easily crosses the placental barrier, and has been shown to influence gene expression during fetal brain development. The purpose of this study was to investigate the effect of in utero BPA exposure on gene expression in the anterior hypothalamus, the basal nucleus of the stria terminalis (BNST), and hippocampus in C57BL/6 mice. Mice were exposed in utero to human-relevant doses of BPA, and then RNA sequencing was performed on male PND 28 tissue from whole hypothalamus (n = 3/group) that included the medial preoptic area (mPOA) and BNST to determine whether any genes were differentially expressed between BPA-exposed and control mice. A subset of genes was selected for further study using RT-qPCR on adult tissue from hippocampus to determine whether any differentially expressed genes (DEGs) persisted into adulthood. Two different RNA-Seq workflows indicated a total of 259 genes that were differentially expressed between BPA-exposed and control mice. Gene ontology analysis indicated that those DEGs were overrepresented in categories relating to mating, cell-cell signaling, behavior, neurodevelopment, neurogenesis, synapse formation, cognition, learning behaviors, hormone activity, and signaling receptor activity, among others. Ingenuity Pathway Analysis was used to interrogate novel gene networks and upstream regulators, indicating the top five upstream regulators as huntingtin, beta-estradiol, alpha-synuclein, Creb1, and estrogen receptor (ER)-alpha. In addition, 15 DE genes were identified that are suspected in autism spectrum disorders.
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26
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Santoro A, Chianese R, Troisi J, Richards S, Nori SL, Fasano S, Guida M, Plunk E, Viggiano A, Pierantoni R, Meccariello R. Neuro-toxic and Reproductive Effects of BPA. Curr Neuropharmacol 2020; 17:1109-1132. [PMID: 31362658 PMCID: PMC7057208 DOI: 10.2174/1570159x17666190726112101] [Citation(s) in RCA: 133] [Impact Index Per Article: 33.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Revised: 06/04/2019] [Accepted: 07/19/2019] [Indexed: 02/08/2023] Open
Abstract
Background: Bisphenol A (BPA) is one of the highest volume chemicals produced worldwide. It has recognized activity as an endocrine-disrupting chemical and has suspected roles as a neurological and reproductive toxicant. It interferes in steroid signaling, induces oxidative stress, and affects gene expression epigenetically. Gestational, perinatal and neonatal exposures to BPA affect developmental processes, including brain development and gametogenesis, with consequences on brain functions, behavior, and fertility. Methods: This review critically analyzes recent findings on the neuro-toxic and reproductive effects of BPA (and its ana-logues), with focus on neuronal differentiation, synaptic plasticity, glia and microglia activity, cognitive functions, and the central and local control of reproduction. Results: BPA has potential human health hazard associated with gestational, peri- and neonatal exposure. Beginning with BPA’s disposition, this review summarizes recent findings on the neurotoxicity of BPA and its analogues, on neuronal dif-ferentiation, synaptic plasticity, neuro-inflammation, neuro-degeneration, and impairment of cognitive abilities. Furthermore, it reports the recent findings on the activity of BPA along the HPG axis, effects on the hypothalamic Gonadotropin Releas-ing Hormone (GnRH), and the associated effects on reproduction in both sexes and successful pregnancy. Conclusion: BPA and its analogues impair neuronal activity, HPG axis function, reproduction, and fertility. Contrasting re-sults have emerged in animal models and human. Thus, further studies are needed to better define their safety levels. This re-view offers new insights on these issues with the aim to find the “fil rouge”, if any, that characterize BPA’s mechanism of action with outcomes on neuronal function and reproduction.
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Affiliation(s)
- Antonietta Santoro
- Department of Medicine, Surgery and Dentistry "Scuola Medica Salernitana", University of Salerno, Baronissi, SA, Italy
| | - Rosanna Chianese
- Department of Experimental Medicine, University of Campania "Luigi Vanvitelli", Caserta, Italy
| | - Jacopo Troisi
- Department of Medicine, Surgery and Dentistry "Scuola Medica Salernitana", University of Salerno, Baronissi, SA, Italy.,Theoreo srl - Spin-off company of the University of Salerno, Salerno, Italy.,European Biomedical Research Institute of Salerno (EBRIS), Salerno, Italy
| | - Sean Richards
- University of Tennessee College of Medicine, Department of Obstetrics and Gynecology, Chattanooga, TN, United States.,Department of Biology, Geology and Environmental Sciences, University of Tennessee at Chattanooga, Chattanooga, TN, United States
| | - Stefania Lucia Nori
- Department of Medicine, Surgery and Dentistry "Scuola Medica Salernitana", University of Salerno, Baronissi, SA, Italy
| | - Silvia Fasano
- Department of Experimental Medicine, University of Campania "Luigi Vanvitelli", Caserta, Italy
| | - Maurizio Guida
- Department of Medicine, Surgery and Dentistry "Scuola Medica Salernitana", University of Salerno, Baronissi, SA, Italy.,Theoreo srl - Spin-off company of the University of Salerno, Salerno, Italy.,European Biomedical Research Institute of Salerno (EBRIS), Salerno, Italy
| | - Elizabeth Plunk
- University of Tennessee College of Medicine, Department of Obstetrics and Gynecology, Chattanooga, TN, United States
| | - Andrea Viggiano
- Department of Medicine, Surgery and Dentistry "Scuola Medica Salernitana", University of Salerno, Baronissi, SA, Italy
| | - Riccardo Pierantoni
- Department of Experimental Medicine, University of Campania "Luigi Vanvitelli", Caserta, Italy
| | - Rosaria Meccariello
- Department of Movement Sciences and Wellbeing, Parthenope University of Naples, Naples, Italy
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Bansal A, Robles-Matos N, Wang PZ, Condon DE, Joshi A, Pinney SE. In utero Bisphenol A Exposure Is Linked with Sex Specific Changes in the Transcriptome and Methylome of Human Amniocytes. J Clin Endocrinol Metab 2020; 105:5571768. [PMID: 31536135 PMCID: PMC7046022 DOI: 10.1210/clinem/dgz037] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/30/2019] [Accepted: 09/17/2019] [Indexed: 12/20/2022]
Abstract
CONTEXT Prenatal exposure to bisphenol A (BPA) is linked to obesity and diabetes but the molecular mechanisms driving these phenomena are not known. Alterations in deoxyribonucleic acid (DNA) methylation in amniocytes exposed to BPA in utero represent a potential mechanism leading to metabolic dysfunction later in life. OBJECTIVE To profile changes in genome-wide DNA methylation and expression in second trimester human amniocytes exposed to BPA in utero. DESIGN A nested case-control study was performed in amniocytes matched for offspring sex, maternal race/ethnicity, maternal age, gestational age at amniocentesis, and gestational age at birth. Cases had amniotic fluid BPA measuring 0.251 to 23.74 ng/mL. Sex-specific genome-wide DNA methylation analysis and RNA-sequencing (RNA-seq) were performed to determine differentially methylated regions (DMRs) and gene expression changes associated with BPA exposure. Ingenuity pathway analysis was performed to identify biologically relevant pathways enriched after BPA exposure. In silico Hi-C analysis identified potential chromatin interactions with DMRs. RESULTS There were 101 genes with altered expression in male amniocytes exposed to BPA (q < 0.05) in utero, with enrichment of pathways critical to hepatic dysfunction, collagen signaling and adipogenesis. Thirty-six DMRs were identified in male BPA-exposed amniocytes and 14 in female amniocyte analysis (q < 0.05). Hi-C analysis identified interactions between DMRs and 24 genes with expression changes in male amniocytes and 12 in female amniocytes (P < 0.05). CONCLUSION In a unique repository of human amniocytes exposed to BPA in utero, sex-specific analyses identified gene expression changes in pathways associated with metabolic disease and novel DMRs with potential distal regulatory functions.
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Affiliation(s)
- Amita Bansal
- Center for Research on Reproduction and Women’s Health, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Center of Excellence in Environmental Toxicology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Nicole Robles-Matos
- Center of Excellence in Environmental Toxicology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Epigenetics Program, Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Paul Zhiping Wang
- Center of Excellence in Environmental Toxicology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Penn Bioinformatics Core, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - David E Condon
- Sanford Health, Sioux Falls, SD, USA
- Penn Bioinformatics Core, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Apoorva Joshi
- Division of Endocrinology and Diabetes, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
| | - Sara E Pinney
- Center for Research on Reproduction and Women’s Health, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Center of Excellence in Environmental Toxicology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Division of Endocrinology and Diabetes, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Correspondence and Reprint Requests: Sara E. Pinney, Division of Endocrinology and Diabetes, Children’s Hospital Philadelphia, 3615 Civic Center Boulevard, Philadelphia, PA 19104, USA. E-mail:
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Zhang G, Byun HR, Ying Z, Blencowe M, Zhao Y, Hong J, Shu L, Chella Krishnan K, Gomez-Pinilla F, Yang X. Differential metabolic and multi-tissue transcriptomic responses to fructose consumption among genetically diverse mice. Biochim Biophys Acta Mol Basis Dis 2020; 1866:165569. [PMID: 31669422 PMCID: PMC6993985 DOI: 10.1016/j.bbadis.2019.165569] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2019] [Revised: 10/05/2019] [Accepted: 10/10/2019] [Indexed: 12/12/2022]
Abstract
Understanding how individuals react differently to the same treatment is a major concern in precision medicine. Metabolic challenges such as the one posed by high fructose intake are important determinants of disease mechanisms. We embarked on studies to determine how fructose affects differential metabolic dysfunctions across genetically dissimilar mice, namely, C57BL/6 J (B6), DBA/2 J (DBA) and FVB/NJ (FVB), by integrating physiological and gene regulatory mechanisms. We report that fructose has strain-specific effects, involving tissue-specific gene regulatory cascades in hypothalamus, liver, and white adipose tissues. DBA mice showed the largest numbers of genes associated with adiposity, congruent with their highest susceptibility to adiposity gain and glucose intolerance across the three tissues. In contrast, B6 and FVB mainly exhibited cholesterol phenotypes, accompanying the largest number of adipose genes correlating with total cholesterol in B6, and liver genes correlating with LDL in FVB mice. Tissue-specific network modeling predicted strain-and tissue-specific regulators such as Fgf21 (DBA) and Lss (B6), which were subsequently validated in primary hepatocytes. Strain-specific fructose-responsive genes revealed susceptibility for human diseases such that genes in liver and adipose tissue in DBA showed strong enrichment for human type 2 diabetes and obesity traits. Liver and adipose genes in FVB were mostly related to lipid traits, and liver and adipose genes in B6 showed relevance to most cardiometabolic traits tested. Our results show that fructose induces gene regulatory pathways that are tissue specific and dependent on the genetic make-up, which may underlie interindividual variability in cardiometabolic responses to high fructose consumption.
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Affiliation(s)
- Guanglin Zhang
- Department of Integrative Biology and Physiology, University of California, Los Angeles, Los Angeles, California 90095, USA
| | - Hyae Ran Byun
- Department of Integrative Biology and Physiology, University of California, Los Angeles, Los Angeles, California 90095, USA
| | - Zhe Ying
- Department of Integrative Biology and Physiology, University of California, Los Angeles, Los Angeles, California 90095, USA
| | - Montgomery Blencowe
- Department of Integrative Biology and Physiology, University of California, Los Angeles, Los Angeles, California 90095, USA
| | - Yuqi Zhao
- Department of Integrative Biology and Physiology, University of California, Los Angeles, Los Angeles, California 90095, USA
| | - Jason Hong
- Department of Integrative Biology and Physiology, University of California, Los Angeles, Los Angeles, California 90095, USA
| | - Le Shu
- Department of Integrative Biology and Physiology, University of California, Los Angeles, Los Angeles, California 90095, USA
| | - Karthick Chella Krishnan
- Department of Medicine/Division of Cardiology and Department of Human Genetics, University of California, Los Angeles, Los Angeles, CA, USA
| | - Fernando Gomez-Pinilla
- Department of Integrative Biology and Physiology, University of California, Los Angeles, Los Angeles, California 90095, USA; Department of Neurosurgery, UCLA Brain Injury Research Center, University of California, Los Angeles, Los Angeles, California 90095, USA.
| | - Xia Yang
- Department of Integrative Biology and Physiology, University of California, Los Angeles, Los Angeles, California 90095, USA; Institute for Quantitative and Computational Biosciences, University of California, Los Angeles, Los Angeles, California 90095, USA; Molecular Biology Institute, University of California, Los Angeles, Los Angeles, California 90095, USA.
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Blencowe M, Karunanayake T, Wier J, Hsu N, Yang X. Network Modeling Approaches and Applications to Unravelling Non-Alcoholic Fatty Liver Disease. Genes (Basel) 2019; 10:E966. [PMID: 31771247 PMCID: PMC6947017 DOI: 10.3390/genes10120966] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Revised: 11/18/2019] [Accepted: 11/22/2019] [Indexed: 12/12/2022] Open
Abstract
Non-alcoholic fatty liver disease (NAFLD) is a progressive condition of the liver encompassing a range of pathologies including steatosis, non-alcoholic steatohepatitis (NASH), cirrhosis, and hepatocellular carcinoma. Research into this disease is imperative due to its rapid growth in prevalence, economic burden, and current lack of FDA approved therapies. NAFLD involves a highly complex etiology that calls for multi-tissue multi-omics network approaches to uncover the pathogenic genes and processes, diagnostic biomarkers, and potential therapeutic strategies. In this review, we first present a basic overview of disease pathogenesis, risk factors, and remaining knowledge gaps, followed by discussions of the need and concepts of multi-tissue multi-omics approaches, various network methodologies and application examples in NAFLD research. We highlight the findings that have been uncovered thus far including novel biomarkers, genes, and biological pathways involved in different stages of NAFLD, molecular connections between NAFLD and its comorbidities, mechanisms underpinning sex differences, and druggable targets. Lastly, we outline the future directions of implementing network approaches to further improve our understanding of NAFLD in order to guide diagnosis and therapeutics.
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Affiliation(s)
- Montgomery Blencowe
- Department of Integrative Biology and Physiology, University of California, Los Angeles, 610 Charles E. Young Drive East, Los Angeles, CA 90095, USA; (M.B.); (T.K.); (J.W.); (N.H.)
- Molecular, Cellular, and Integrative Physiology Interdepartmental Program, University of California, Los Angeles, 610 Charles E. Young Drive East, Los Angeles, CA 90095, USA
| | - Tilan Karunanayake
- Department of Integrative Biology and Physiology, University of California, Los Angeles, 610 Charles E. Young Drive East, Los Angeles, CA 90095, USA; (M.B.); (T.K.); (J.W.); (N.H.)
| | - Julian Wier
- Department of Integrative Biology and Physiology, University of California, Los Angeles, 610 Charles E. Young Drive East, Los Angeles, CA 90095, USA; (M.B.); (T.K.); (J.W.); (N.H.)
| | - Neil Hsu
- Department of Integrative Biology and Physiology, University of California, Los Angeles, 610 Charles E. Young Drive East, Los Angeles, CA 90095, USA; (M.B.); (T.K.); (J.W.); (N.H.)
| | - Xia Yang
- Department of Integrative Biology and Physiology, University of California, Los Angeles, 610 Charles E. Young Drive East, Los Angeles, CA 90095, USA; (M.B.); (T.K.); (J.W.); (N.H.)
- Molecular, Cellular, and Integrative Physiology Interdepartmental Program, University of California, Los Angeles, 610 Charles E. Young Drive East, Los Angeles, CA 90095, USA
- Interdepartmental Program of Bioinformatics, University of California, Los Angeles, 610 Charles E. Young Drive East, Los Angeles, CA 90095, USA
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Qing-Xian L, Lin-Long W, Yi-Zhong W, Liang L, Hui H, Liao-Bin C, Hui W. Programming changes in GLUT1 mediated the accumulation of AGEs and matrix degradation in the articular cartilage of female adult rats after prenatal caffeine exposure. Pharmacol Res 2019; 151:104555. [PMID: 31765739 DOI: 10.1016/j.phrs.2019.104555] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/29/2019] [Revised: 11/12/2019] [Accepted: 11/18/2019] [Indexed: 12/15/2022]
Abstract
Osteoarthritis is associated with intrauterine growth retardation (IUGR) and abnormal glucose metabolism. Our laboratory previously reported that prenatal caffeine exposure (PCE) can induce intrauterine maternal glucocorticoid (GC) overexposure in IUGR offspring and increase susceptibility to osteoarthritis after birth. In the present study, we demonstrated the essential role of glucose transporter 1 (GLUT1) programming changes in the increased matrix degradation of articular cartilage and susceptibility to osteoarthritis in female PCE adult offspring. In vivo, we found that PCE decreased the matrix content but did not significantly change the expression of matrix degradation-related genes in the articular cartilage of female fetal rats. The decreased expression of IGF1 and GLUT1 and the content of advanced-glycation-end-products (AGEs) were also detected. At different postnatal stages (2, 6, and 12 weeks), the cartilage matrix content decreased while the degradation-related genes expression increased in the PCE group. Meanwhile, the expression of IGF1 and GLUT1 and AGEs content in the local cartilage increased. In vitro, the expression levels of IGF1 and GLUT1 were inhibited by corticosterone but remained unchanged under caffeine treatment. Exogenous IGF1 can reverse the corticosterone-induced decrease in GLUT1 expression and promote AGEs production, while mifepristone (a glucocorticoid receptor inhibitor) reversed the corticosterone-induced low expression of IGF1 and GLUT1. Exogenous AGEs can increase the expression of inflammatory factors (IL-6 and TNF-α) and degradation-related genes, and decrease the matrix synthesis-related genes expression in chondrocyte. In conclusion, the GC-IGF1-GLUT1 axis mediated intrauterine dysplasia of articular cartilage, increased accumulation of AGEs and matrix degradation after birth in PCE female offspring, thereby increasing their susceptibility to osteoarthritis in adulthood.
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Affiliation(s)
- Li Qing-Xian
- Department of Orthopedic Surgery, Zhongnan Hospital of Wuhan University, Wuhan, 430071, China
| | - Wang Lin-Long
- Department of Orthopedic Surgery, Zhongnan Hospital of Wuhan University, Wuhan, 430071, China; Hubei Provincial Key Laboratory of Developmentally Originated Disease, Wuhan, 430071, China
| | - Wang Yi-Zhong
- Department of Orthopedic Surgery, Zhongnan Hospital of Wuhan University, Wuhan, 430071, China
| | - Liu Liang
- Department of Orthopedic Surgery, Zhongnan Hospital of Wuhan University, Wuhan, 430071, China
| | - Han Hui
- Department of Orthopedic Surgery, Zhongnan Hospital of Wuhan University, Wuhan, 430071, China
| | - Chen Liao-Bin
- Department of Orthopedic Surgery, Zhongnan Hospital of Wuhan University, Wuhan, 430071, China; Hubei Provincial Key Laboratory of Developmentally Originated Disease, Wuhan, 430071, China.
| | - Wang Hui
- Department of Pharmacology, Basic Medical School of Wuhan University, Wuhan, 430071, China; Hubei Provincial Key Laboratory of Developmentally Originated Disease, Wuhan, 430071, China.
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Blencowe M, Arneson D, Ding J, Chen YW, Saleem Z, Yang X. Network modeling of single-cell omics data: challenges, opportunities, and progresses. Emerg Top Life Sci 2019; 3:379-398. [PMID: 32270049 PMCID: PMC7141415 DOI: 10.1042/etls20180176] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2019] [Revised: 06/07/2019] [Accepted: 06/24/2019] [Indexed: 01/07/2023]
Abstract
Single-cell multi-omics technologies are rapidly evolving, prompting both methodological advances and biological discoveries at an unprecedented speed. Gene regulatory network modeling has been used as a powerful approach to elucidate the complex molecular interactions underlying biological processes and systems, yet its application in single-cell omics data modeling has been met with unique challenges and opportunities. In this review, we discuss these challenges and opportunities, and offer an overview of the recent development of network modeling approaches designed to capture dynamic networks, within-cell networks, and cell-cell interaction or communication networks. Finally, we outline the remaining gaps in single-cell gene network modeling and the outlooks of the field moving forward.
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Affiliation(s)
- Montgomery Blencowe
- Department of Integrative Biology and Physiology, University of California, Los Angeles, 610 Charles E. Young Drive East, Los Angeles, CA 90095, U.S.A
| | - Douglas Arneson
- Department of Integrative Biology and Physiology, University of California, Los Angeles, 610 Charles E. Young Drive East, Los Angeles, CA 90095, U.S.A
- Bioinformatics Interdepartmental Program, University of California, Los Angeles, 610 Charles E. Young Drive East, Los Angeles, CA 90095, U.S.A
| | - Jessica Ding
- Department of Integrative Biology and Physiology, University of California, Los Angeles, 610 Charles E. Young Drive East, Los Angeles, CA 90095, U.S.A
| | - Yen-Wei Chen
- Department of Integrative Biology and Physiology, University of California, Los Angeles, 610 Charles E. Young Drive East, Los Angeles, CA 90095, U.S.A
- Molecular Toxicology Program, University of California, Los Angeles, 610 Charles E. Young Drive East, Los Angeles, CA 90095, U.S.A
| | - Zara Saleem
- Department of Integrative Biology and Physiology, University of California, Los Angeles, 610 Charles E. Young Drive East, Los Angeles, CA 90095, U.S.A
| | - Xia Yang
- Department of Integrative Biology and Physiology, University of California, Los Angeles, 610 Charles E. Young Drive East, Los Angeles, CA 90095, U.S.A
- Bioinformatics Interdepartmental Program, University of California, Los Angeles, 610 Charles E. Young Drive East, Los Angeles, CA 90095, U.S.A
- Molecular Toxicology Program, University of California, Los Angeles, 610 Charles E. Young Drive East, Los Angeles, CA 90095, U.S.A
- Institute for Quantitative and Computational Biosciences, University of California, Los Angeles, 610 Charles E. Young Drive East, Los Angeles, CA 90095, U.S.A
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32
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Shu L, Meng Q, Diamante G, Tsai B, Chen YW, Mikhail A, Luk H, Ritz B, Allard P, Yang X. Prenatal Bisphenol A Exposure in Mice Induces Multitissue Multiomics Disruptions Linking to Cardiometabolic Disorders. Endocrinology 2019; 160:409-429. [PMID: 30566610 PMCID: PMC6349005 DOI: 10.1210/en.2018-00817] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/16/2018] [Accepted: 12/13/2018] [Indexed: 12/21/2022]
Abstract
The health impacts of endocrine-disrupting chemicals (EDCs) remain debated, and their tissue and molecular targets are poorly understood. In this study, we leveraged systems biology approaches to assess the target tissues, molecular pathways, and gene regulatory networks associated with prenatal exposure to the model EDC bisphenol A (BPA). Prenatal BPA exposure at 5 mg/kg/d, a dose below most reported no-observed-adverse-effect levels, led to tens to thousands of transcriptomic and methylomic alterations in the adipose, hypothalamus, and liver tissues in male offspring in mice, with cross-tissue perturbations in lipid metabolism as well as tissue-specific alterations in histone subunits, glucose metabolism, and extracellular matrix. Network modeling prioritized main molecular targets of BPA, including Pparg, Hnf4a, Esr1, Srebf1, and Fasn as well as numerous less studied targets such as Cyp51 and long noncoding RNAs across tissues, Fa2h in hypothalamus, and Nfya in adipose tissue. Lastly, integrative analyses identified the association of BPA molecular signatures with cardiometabolic phenotypes in mouse and human. Our multitissue, multiomics investigation provides strong evidence that BPA perturbs diverse molecular networks in central and peripheral tissues and offers insights into the molecular targets that link BPA to human cardiometabolic disorders.
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Affiliation(s)
- Le Shu
- Department of Integrative Biology and Physiology, University of California, Los Angeles, Los Angeles, California
- Molecular, Cellular, and Integrative Physiology Interdepartmental Program, University of California, Los Angeles, Los Angeles, California
| | - Qingying Meng
- Department of Integrative Biology and Physiology, University of California, Los Angeles, Los Angeles, California
| | - Graciel Diamante
- Department of Integrative Biology and Physiology, University of California, Los Angeles, Los Angeles, California
| | - Brandon Tsai
- Department of Integrative Biology and Physiology, University of California, Los Angeles, Los Angeles, California
| | - Yen-Wei Chen
- Molecular Toxicology Interdepartmental Program, University of California, Los Angeles, Los Angeles, California
| | - Andrew Mikhail
- Department of Integrative Biology and Physiology, University of California, Los Angeles, Los Angeles, California
| | - Helen Luk
- Department of Integrative Biology and Physiology, University of California, Los Angeles, Los Angeles, California
| | - Beate Ritz
- Department of Epidemiology, Fielding School of Public Health, University of California, Los Angeles, Los Angeles, California
- Institute for Society and Genetics, University of California, Los Angeles, Los Angeles, California
| | - Patrick Allard
- Molecular Toxicology Interdepartmental Program, University of California, Los Angeles, Los Angeles, California
- Institute for Society and Genetics, University of California, Los Angeles, Los Angeles, California
| | - Xia Yang
- Department of Integrative Biology and Physiology, University of California, Los Angeles, Los Angeles, California
- Molecular, Cellular, and Integrative Physiology Interdepartmental Program, University of California, Los Angeles, Los Angeles, California
- Molecular Toxicology Interdepartmental Program, University of California, Los Angeles, Los Angeles, California
- Institute for Quantitative and Computational Biosciences, University of California, Los Angeles, Los Angeles, California
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